[Freesurfer] mris_preproc

2012-06-05 Thread Richter, Julia
Dear FreeSurfer experts, I am trying to run mris_preproc after caching my data. As command lines, I am typing: mris_preproc --fsgd file.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi lh \ --out lh.allpatients.thickness10.mgh Everytime I am trying to run these commands,

Re: [Freesurfer] mris_preproc

2012-06-05 Thread Richter, Julia
Could it be that the mris_preproc and the mri_glmfit file are missing in my freesurfer package? If so, can anybody send them to me? Thank you very much, Julia Von: Richter, Julia Gesendet: Dienstag, 5. Juni 2012 10:11 Bis: freesurfer@nmr.mgh.harvard.edu Betreff:

Re: [Freesurfer] Correction of registration in preproc-sess stream

2012-06-05 Thread Jörg Pfannmöller
Dear Doug, I am having a partial field of view and a full brain scan. How can I integrate the results in the preproc-sess sequence in order to complete the preprocessing correctly? Cheers pfannmoe On Mon, 04 Jun 2012 11:42:32 -0400 Douglas N Greve wrote: > You can try running register-sess

Re: [Freesurfer] mris_preproc

2012-06-05 Thread Bruce Fischl
Hi Julia that seems unlikely. What happens when you type: ls $FREESURFER_HOME/bin/mris_preproc cheers Bruce On Tue, 5 Jun 2012, Richter, Julia wrote: > Could it be that the mris_preproc and the mri_glmfit file are missing in my > freesurfer package? If so, can anybody send them to me? > > Tha

[Freesurfer] MNI to RAS surface coordinates

2012-06-05 Thread Yolanda Vives
Dear Freesurfer experts, I have performed a VBM analysis with SPM, using some VOIs. Now I would like to compare the volumetric results obtained with SPM with those of cortical thickness obtained with Freesurfer in the same VOIs (approximately). For this purpose, I would like to transform the MNI

Re: [Freesurfer] mris_preproc

2012-06-05 Thread Richter, Julia
after typing your command in my terminal window, it appears: /usr/local/freesurfer/bin/mris_preproc Von: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Gesendet: Dienstag, 5. Juni 2012 15:05 Bis: Richter, Julia Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [F

Re: [Freesurfer] mris_preproc

2012-06-05 Thread Bruce Fischl
okay, how about: which mris_preproc and just mris_preproc On Tue, 5 Jun 2012, Richter, Julia wrote: > after typing your command in my terminal window, it appears: > > /usr/local/freesurfer/bin/mris_preproc > > Von: Bruce Fischl [fis...@nmr.mgh.harvard.e

Re: [Freesurfer] mris_preproc

2012-06-05 Thread Richter, Julia
nothing happens when typing "which mris_prepoc", command not found when typing only "mris_preproc" Von: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Gesendet: Dienstag, 5. Juni 2012 15:25 Bis: Richter, Julia Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: AW:

Re: [Freesurfer] mris_preproc

2012-06-05 Thread Bruce Fischl
so your path must be wrong then. Are you sourcing $FREESURFER_HOME/FreeSurferEnv.csh? That is, in your .login or .cshrc or whatever gets run at startup do you do: source $FREESURFER_HOME/FreeSurferEnv.csh try running that at the command line and see if it finds mris_preproc afterwards. cheers

[Freesurfer] aparc+aseg labels

2012-06-05 Thread Sarosh, Cyrus
Hello, I was hoping somebody could help me out. I am trying to create a label file for the aparc+aseg file. All I'm wanting is the pixel value and the label. I know there is the FreeSurferColorLUT.txt file which contains this information, but looking at this file I can tell that all of these la

Re: [Freesurfer] aparc+aseg labels

2012-06-05 Thread Lilla Zollei
Hi Cyrus, You can run the following script: compute_label_volumes.csh It will list all the labels that are in your segmentation file (and also tell you the number of voxels colored by this label and th etotal volume). Lilla On Tue, 5 Jun 2012, Sarosh, Cyrus wrote: Hello,   I was hopin

Re: [Freesurfer] using own average subject

2012-06-05 Thread Schuster, Christina /DZNE
Hi, what would you consider a small sample? I have one sample of 40 participants (20 patients, 20 controls) for that I thought it would be best to use the fsaverage and then maybe display it on my own subjects average. The other study consists of roughly 140 participants (1/3 are healthy con

Re: [Freesurfer] Correction of registration in preproc-sess stream

2012-06-05 Thread Douglas Greve
You can't do directly from preproc-sess, but you can do it from register-sess if you have an additional whole brain acquisition in the same session. This can be any acquisition (BOLD, MPRAGE, low-b DTI, etc) as long as it is whole brain. If your anatomical was acquired in the same session, then

Re: [Freesurfer] freesurfer question

2012-06-05 Thread Douglas Greve
Hi Tony, you can use bbregister to create the registration file. You might also look at the multi-modal tutorial on our wiki as this goes over the steps that you will need to get and apply the registration. For the 2nd question, you can use mris_anatomical_stats. dou

[Freesurfer] acquiring substancia nigra volume

2012-06-05 Thread Zohra Ahmadzai
The final recon process, autorecon3 - uses "ASegStatsLUT.txt" by default to segment certain subcortical structures listed within this textfile. On the otherhand, FreeSurferColorLUT.txt has labels for more subregions, including the substancia nigra which is a region of interest for a particular

Re: [Freesurfer] acquiring substancia nigra volume

2012-06-05 Thread Bruce Fischl
not currently, sorry On Wed, 6 Jun 2012, Zohra Ahmadzai wrote: > > The final recon process, autorecon3 - uses "ASegStatsLUT.txt" by default to > segment certain subcortical structures listed within this textfile. > > On the otherhand, FreeSurferColorLUT.txt has labels for more subregions, > incl

[Freesurfer] How to avoid overlaps between volume labels?

2012-06-05 Thread Yuko Yotsumoto
Hello, With FreeSurfer v4.5, I have three functionally localized surface labels (A.label, B.label, C.label), and converted this label to volume by using mri_label2vol with --proj. I now have three volume labels, A.mgz, B.mgz, and C.mgz. Because these three labels are adjacent to each other, [